Package picard.illumina.parser
Class PerTileOrPerRunFileUtil
- java.lang.Object
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- picard.illumina.parser.ParameterizedFileUtil
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- picard.illumina.parser.PerTileFileUtil
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- picard.illumina.parser.PerTileOrPerRunFileUtil
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public class PerTileOrPerRunFileUtil extends PerTileFileUtil
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Field Summary
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Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
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Constructor Summary
Constructors Constructor Description PerTileOrPerRunFileUtil(String extension, File base, FileFaker faker, int lane)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
checkTileCount()
boolean
filesAvailable()
Determine whether or not files are availablevoid
setTilesForPerRunFile(List<Integer> tiles)
List<String>
verify(List<Integer> expectedTiles, int[] expectedCycles)
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files-
Methods inherited from class picard.illumina.parser.PerTileFileUtil
fakeFiles, getFiles, getFiles
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Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
escapePeriods, fileToTile, getRunFile, getTiledFiles, getTiles, makeBarcodeRegex, makeLaneTileRegex, setTiles
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Method Detail
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filesAvailable
public boolean filesAvailable()
Description copied from class:ParameterizedFileUtil
Determine whether or not files are available- Overrides:
filesAvailable
in classPerTileFileUtil
- Returns:
- return true if files are found matching this types pattern, false otherwise
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setTilesForPerRunFile
public void setTilesForPerRunFile(List<Integer> tiles)
- Overrides:
setTilesForPerRunFile
in classParameterizedFileUtil
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checkTileCount
public boolean checkTileCount()
- Overrides:
checkTileCount
in classParameterizedFileUtil
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verify
public List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
Description copied from class:ParameterizedFileUtil
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files- Overrides:
verify
in classPerTileFileUtil
- Parameters:
expectedTiles
- An ordered list of tile numbersexpectedCycles
- An ordered list of cycle numbers that may contain gaps- Returns:
- A list of error messages for this format
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